Yes, select the desired ones from the list at the bottom left that you wish to be included in the recording. If you use a few different setups, though, it can be easy to forget to re-select any you had de-selected!
What I did to get around my “human error” issues was to have certain “standardized” shows I used as templates by making them be unique cantabile instances, and those would have all the recording ports selected in the lower left already so I did not have to ever go in there again. See this post to understand how that is done.
What I do is I create a multi-config and open it so it makes default prefs, then close it and replace its prefs with a basic set that has all my ports already. I then open it and customize it to my new requirements.
If that isn’t clear - open the version you want to get the prefs from, go to Tools=>Open Preferences Folder (or just go to C:\Users\yourprofile\AppData\Local\Topten Software), copy settings.json (and maybe plugins.json + plugins.user.json) and paste those into your new configuration’s folder replacing the others. The rest is easy-peasy! Open it up, load a song or create on, and have fun!
Using that method all the ports you’d created before are already typed in.